Turning the CXA amp off/on again quickly will mean the amps are still powered. This is because when you switch off an amp, the power doesn't suddenly disappear. There will be voltage left in the large capacitors that will gradually drain away. If you switch the amp back on again while it is still in this 'powered' state (voltage hasn't completely drained from the capacitors) then the amp won't be powering up in the same way as it would be from standby, and depending on which parts of the circuit are still powered with the residual charge will change what actually causes the issue in terms of which protection system might get triggered.
For example, if there is still power in the amplifier circuits, the power on checks may see some DC apparent, or if there is some power in the signal circuit it may be power on the input to the amp stage that may be seen as clipping.
This is expected behaviour, but should not be seen by the majority of normal users and long presses of the IR button shouldn't power the unit on/off in quick succession, but two separate presses will. It is for this reason that we do not recommend quickly powering the unit off and on again in quick succession as it could cause the CAP5 protection system to be triggered.